[
https://issues.apache.org/jira/browse/ARROW-17252?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17573068#comment-17573068
]
Dewey Dunnington edited comment on ARROW-17252 at 7/29/22 5:17 PM:
-------------------------------------------------------------------
I can get a similar leak locally, too using a dockerfile:
{noformat}
FROM ubuntu:20.04
ARG DEBIAN_FRONTEND=noninteractive
ENV TZ=America/Halifax
RUN apt-get update && apt-get install -y valgrind r-base cmake git libxml2-dev
libcurl4-openssl-dev libssl-dev libgit2-dev libfontconfig1-dev libfreetype6-dev
libharfbuzz-dev libfribidi-dev libpng-dev libtiff5-dev libjpeg-dev
RUN git clone https://github.com/apache/arrow.git /arrow && mkdir /arrow-build
&& cd /arrow-build && cmake /arrow/cpp -DARROW_CSV=ON -DARROW_FILESYSTEM=ON
-DARROW_COMPUTE=ON -DBoost_SOURCE=BUNDLED && cmake --build . && cmake --install
. --prefix /arrow-dist
RUN R -e 'install.packages(c("devtools", "cpp11", "R6", "assertthat", "bit64",
"bit", "cli", "ellipsis", "glue", "magrittr", "purrr", "rlang", "tidyselect",
"vctrs", "lubridate", "dplyr", "hms"), repos = "https://cloud.r-project.org";)'
ENV ARROW_HOME /arrow-dist
ENV LD_LIBRARY_PATH /arrow-dist/lib
RUN cd /arrow/r && R CMD INSTALL .
{noformat}
Launching R with valgrind:
{noformat}
R -d "valgrind --tool=memcheck --leak-check=full"
{noformat}
...and I get this leak:
{noformat}
==387== 2,608 (72 direct, 2,536 indirect) bytes in 1 blocks are definitely lost
in loss record 625 of 4,108
==387== at 0x484A3C4: operator new(unsigned long) (in
/usr/lib/aarch64-linux-gnu/valgrind/vgpreload_memcheck-arm64-linux.so)
==387== by 0x1566648F:
arrow::Table::FromRecordBatches(std::shared_ptr<arrow::Schema>,
std::vector<std::shared_ptr<arrow::RecordBatch>,
std::allocator<std::shared_ptr<arrow::RecordBatch> > > const&) (in
/arrow-dist/lib/libarrow.so.900.0.0)
==387== by 0x15629FB7: arrow::RecordBatchReader::ToTable() (in
/arrow-dist/lib/libarrow.so.900.0.0)
==387== by 0x1501C503: operator() (compute-exec.cpp:147)
==387== by 0x1501C503:
std::_Function_handler<arrow::Result<std::shared_ptr<arrow::Table> > (),
ExecPlan_read_table(std::shared_ptr<arrow::compute::ExecPlan> const&,
std::shared_ptr<arrow::compute::ExecNode> const&, cpp11::r_vector<SEXPREC*>,
cpp11::r_vector<cpp11::r_string>,
long)::{lambda()#1}>::_M_invoke(std::_Any_data const&) (std_function.h:286)
==387== by 0x15023427:
std::function<arrow::Result<std::shared_ptr<arrow::Table> > ()>::operator()()
const (std_function.h:688)
==387== by 0x1502352F:
operator()<std::function<arrow::Result<std::shared_ptr<arrow::Table> >()>&>
(future.h:150)
==387== by 0x1502352F: __invoke_impl<void, arrow::detail::ContinueFuture&,
arrow::Future<std::shared_ptr<arrow::Table> >&,
std::function<arrow::Result<std::shared_ptr<arrow::Table> >()>&> (invoke.h:60)
==387== by 0x1502352F: __invoke<arrow::detail::ContinueFuture&,
arrow::Future<std::shared_ptr<arrow::Table> >&,
std::function<arrow::Result<std::shared_ptr<arrow::Table> >()>&> (invoke.h:95)
==387== by 0x1502352F: __call<void, 0, 1> (functional:400)
==387== by 0x1502352F: operator()<> (functional:484)
==387== by 0x1502352F: arrow::internal::FnOnce<void
()>::FnImpl<std::_Bind<arrow::detail::ContinueFuture
(arrow::Future<std::shared_ptr<arrow::Table> >,
std::function<arrow::Result<std::shared_ptr<arrow::Table> > ()>)> >::invoke()
(functional.h:152)
==387== by 0x1579636B:
std::thread::_State_impl<std::thread::_Invoker<std::tuple<arrow::internal::ThreadPool::LaunchWorkersUnlocked(int)::{lambda()#1}>
> >::_M_run() (in /arrow-dist/lib/libarrow.so.900.0.0)
==387== by 0x71F4FAB: ??? (in /usr/lib/aarch64-linux-gnu/libstdc++.so.6.0.28)
==387== by 0x55F1623: start_thread (pthread_create.c:477)
==387== by 0x4DA949B: thread_start (clone.S:78)
{noformat}
(Although this dockerfile doesn't use r-devel...it uses R 3.6 which is a bit
old).
was (Author: paleolimbot):
I can get a similar leak locally, too using a dockerfile:
{noformat}
FROM ubuntu:20.04
ARG DEBIAN_FRONTEND=noninteractive
ENV TZ=America/Halifax
RUN apt-get update && apt-get install -y valgrind r-base cmake git libxml2-dev
libcurl4-openssl-dev libssl-dev libgit2-dev libfontconfig1-dev libfreetype6-dev
libharfbuzz-dev libfribidi-dev libpng-dev libtiff5-dev libjpeg-dev
RUN git clone https://github.com/apache/arrow.git /arrow && mkdir /arrow-build
&& cd /arrow-build && cmake /arrow/cpp -DARROW_CSV=ON -DARROW_DATASET=ON
-DARROW_FILESYSTEM=ON -DARROW_COMPUTE=ON -DBoost_SOURCE=BUNDLED && cmake
--build . && cmake --install . --prefix /arrow-dist
RUN R -e 'install.packages(c("devtools", "cpp11", "R6", "assertthat", "bit64",
"bit", "cli", "ellipsis", "glue", "magrittr", "purrr", "rlang", "tidyselect",
"vctrs", "lubridate", "dplyr", "hms"), repos = "https://cloud.r-project.org";)'
ENV ARROW_HOME /arrow-dist
ENV LD_LIBRARY_PATH /arrow-dist/lib
RUN cd /arrow/r && R CMD INSTALL .
{noformat}
Launching R with valgrind:
{noformat}
R -d "valgrind --tool=memcheck --leak-check=full"
{noformat}
...and I get this leak:
{noformat}
==387== 2,608 (72 direct, 2,536 indirect) bytes in 1 blocks are definitely lost
in loss record 625 of 4,108
==387== at 0x484A3C4: operator new(unsigned long) (in
/usr/lib/aarch64-linux-gnu/valgrind/vgpreload_memcheck-arm64-linux.so)
==387== by 0x1566648F:
arrow::Table::FromRecordBatches(std::shared_ptr<arrow::Schema>,
std::vector<std::shared_ptr<arrow::RecordBatch>,
std::allocator<std::shared_ptr<arrow::RecordBatch> > > const&) (in
/arrow-dist/lib/libarrow.so.900.0.0)
==387== by 0x15629FB7: arrow::RecordBatchReader::ToTable() (in
/arrow-dist/lib/libarrow.so.900.0.0)
==387== by 0x1501C503: operator() (compute-exec.cpp:147)
==387== by 0x1501C503:
std::_Function_handler<arrow::Result<std::shared_ptr<arrow::Table> > (),
ExecPlan_read_table(std::shared_ptr<arrow::compute::ExecPlan> const&,
std::shared_ptr<arrow::compute::ExecNode> const&, cpp11::r_vector<SEXPREC*>,
cpp11::r_vector<cpp11::r_string>,
long)::{lambda()#1}>::_M_invoke(std::_Any_data const&) (std_function.h:286)
==387== by 0x15023427:
std::function<arrow::Result<std::shared_ptr<arrow::Table> > ()>::operator()()
const (std_function.h:688)
==387== by 0x1502352F:
operator()<std::function<arrow::Result<std::shared_ptr<arrow::Table> >()>&>
(future.h:150)
==387== by 0x1502352F: __invoke_impl<void, arrow::detail::ContinueFuture&,
arrow::Future<std::shared_ptr<arrow::Table> >&,
std::function<arrow::Result<std::shared_ptr<arrow::Table> >()>&> (invoke.h:60)
==387== by 0x1502352F: __invoke<arrow::detail::ContinueFuture&,
arrow::Future<std::shared_ptr<arrow::Table> >&,
std::function<arrow::Result<std::shared_ptr<arrow::Table> >()>&> (invoke.h:95)
==387== by 0x1502352F: __call<void, 0, 1> (functional:400)
==387== by 0x1502352F: operator()<> (functional:484)
==387== by 0x1502352F: arrow::internal::FnOnce<void
()>::FnImpl<std::_Bind<arrow::detail::ContinueFuture
(arrow::Future<std::shared_ptr<arrow::Table> >,
std::function<arrow::Result<std::shared_ptr<arrow::Table> > ()>)> >::invoke()
(functional.h:152)
==387== by 0x1579636B:
std::thread::_State_impl<std::thread::_Invoker<std::tuple<arrow::internal::ThreadPool::LaunchWorkersUnlocked(int)::{lambda()#1}>
> >::_M_run() (in /arrow-dist/lib/libarrow.so.900.0.0)
==387== by 0x71F4FAB: ??? (in /usr/lib/aarch64-linux-gnu/libstdc++.so.6.0.28)
==387== by 0x55F1623: start_thread (pthread_create.c:477)
==387== by 0x4DA949B: thread_start (clone.S:78)
{noformat}
(Although this dockerfile doesn't use r-devel...it uses R 3.6 which is a bit
old).
> [R] Intermittent valgrind failure
> ---------------------------------
>
> Key: ARROW-17252
> URL: https://issues.apache.org/jira/browse/ARROW-17252
> Project: Apache Arrow
> Issue Type: Improvement
> Components: R
> Reporter: Dewey Dunnington
> Priority: Major
> Labels: pull-request-available
> Time Spent: 40m
> Remaining Estimate: 0h
>
> A number of recent nightly builds have intermittent failures with valgrind,
> which fails because of possibly leaked memory around an exec plan. This seems
> related to a change in XXX that separated {{ExecPlan_prepare()}} from
> {{ExecPlan_run()}} and added a {{ExecPlan_read_table()}} that uses
> {{RunWithCapturedR()}}. The reported leaks vary but include ExecPlans and
> ExecNodes and fields of those objects.
> A failed run:
> https://dev.azure.com/ursacomputing/crossbow/_build/results?buildId=30310&view=logs&j=0da5d1d9-276d-5173-c4c4-9d4d4ed14fdb&t=d9b15392-e4ce-5e4c-0c8c-b69645229181&l=24980
> Some example output:
> {noformat}
> ==5249== 14,112 (384 direct, 13,728 indirect) bytes in 1 blocks are
> definitely lost in loss record 1,988 of 3,883
> ==5249== at 0x4849013: operator new(unsigned long) (in
> /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so)
> ==5249== by 0x10B2902B:
> std::_Function_handler<arrow::Result<arrow::compute::ExecNode*>
> (arrow::compute::ExecPlan*, std::vector<arrow::compute::ExecNode*,
> std::allocator<arrow::compute::ExecNode*> >, arrow::compute::ExecNodeOptions
> const&),
> arrow::compute::internal::RegisterAggregateNode(arrow::compute::ExecFactoryRegistry*)::{lambda(arrow::compute::ExecPlan*,
> std::vector<arrow::compute::ExecNode*,
> std::allocator<arrow::compute::ExecNode*> >, arrow::compute::ExecNodeOptions
> const&)#1}>::_M_invoke(std::_Any_data const&, arrow::compute::ExecPlan*&&,
> std::vector<arrow::compute::ExecNode*,
> std::allocator<arrow::compute::ExecNode*> >&&,
> arrow::compute::ExecNodeOptions const&) (exec_plan.h:60)
> ==5249== by 0xFA83A0C:
> std::function<arrow::Result<arrow::compute::ExecNode*>
> (arrow::compute::ExecPlan*, std::vector<arrow::compute::ExecNode*,
> std::allocator<arrow::compute::ExecNode*> >, arrow::compute::ExecNodeOptions
> const&)>::operator()(arrow::compute::ExecPlan*,
> std::vector<arrow::compute::ExecNode*,
> std::allocator<arrow::compute::ExecNode*> >, arrow::compute::ExecNodeOptions
> const&) const (std_function.h:622)
> ==5249== 14,528 (160 direct, 14,368 indirect) bytes in 1 blocks are
> definitely lost in loss record 1,989 of 3,883
> ==5249== at 0x4849013: operator new(unsigned long) (in
> /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so)
> ==5249== by 0x10096CB7: arrow::FutureImpl::Make() (future.cc:187)
> ==5249== by 0xFCB6F9A: arrow::Future<arrow::internal::Empty>::Make()
> (future.h:420)
> ==5249== by 0x101AE927: ExecPlanImpl (exec_plan.cc:50)
> ==5249== by 0x101AE927:
> arrow::compute::ExecPlan::Make(arrow::compute::ExecContext*,
> std::shared_ptr<arrow::KeyValueMetadata const>) (exec_plan.cc:355)
> ==5249== by 0xFA77BA2: ExecPlan_create(bool) (compute-exec.cpp:45)
> ==5249== by 0xF9FAE9F: _arrow_ExecPlan_create (arrowExports.cpp:868)
> ==5249== by 0x4953B60: R_doDotCall (dotcode.c:601)
> ==5249== by 0x49C2C16: bcEval (eval.c:7682)
> ==5249== by 0x499DB95: Rf_eval (eval.c:748)
> ==5249== by 0x49A0904: R_execClosure (eval.c:1918)
> ==5249== by 0x49A05B7: Rf_applyClosure (eval.c:1844)
> ==5249== by 0x49B2122: bcEval (eval.c:7094)
> ==5249==
> ==5249== 36,322 (416 direct, 35,906 indirect) bytes in 1 blocks are
> definitely lost in loss record 2,929 of 3,883
> ==5249== at 0x4849013: operator new(unsigned long) (in
> /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so)
> ==5249== by 0x10214F92: arrow::compute::TaskScheduler::Make()
> (task_util.cc:421)
> ==5249== by 0x101AEA6C: ExecPlanImpl (exec_plan.cc:50)
> ==5249== by 0x101AEA6C:
> arrow::compute::ExecPlan::Make(arrow::compute::ExecContext*,
> std::shared_ptr<arrow::KeyValueMetadata const>) (exec_plan.cc:355)
> ==5249== by 0xFA77BA2: ExecPlan_create(bool) (compute-exec.cpp:45)
> ==5249== by 0xF9FAE9F: _arrow_ExecPlan_create (arrowExports.cpp:868)
> ==5249== by 0x4953B60: R_doDotCall (dotcode.c:601)
> ==5249== by 0x49C2C16: bcEval (eval.c:7682)
> ==5249== by 0x499DB95: Rf_eval (eval.c:748)
> ==5249== by 0x49A0904: R_execClosure (eval.c:1918)
> ==5249== by 0x49A05B7: Rf_applyClosure (eval.c:1844)
> ==5249== by 0x49B2122: bcEval (eval.c:7094)
> ==5249== by 0x499DB95: Rf_eval (eval.c:748)
> {noformat}
> We also occasionally get leaked Schemas, and in one case a leaked InputType
> that seemed completely unrelated to the other leaks (ARROW-17225).
> I'm wondering if these have to do with references in lambdas that get passed
> by reference? Or perhaps a cache issue? There were some instances in previous
> leaks where the backtrace to the {{new}} allocator was different between
> reported leaks.
--
This message was sent by Atlassian Jira
(v8.20.10#820010)
